source: branches/lib/HELP_SOURCE/source/concatenate.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB         split.hlp
7
8# format described in ../help.readme
9
10TITLE       Concatenation of sequences
11
12DESCRIPTION
13
14            With the help of the concatenation function, one can concatenate the aligned
15            sequences, which are contained in the same species preserving the ALIGNMENT.
16            Before using concatenation function make sure that the species contains more
17            than two aligned or unaligned sequences.
18
19            Specify a name for the newly created concatenated alignment in the field
20            "New alignment name".
21
22            Use "Sequence Type" button to display the desired type of alignments/sequences
23            from the database.
24
25            Use Arrow buttons (located in between the lists) to select or remove the
26            alignments into/from the "Alignments to be concatenated" list.
27
28            You can also rearrange the order of concatenation of alignments by using "up"
29            and "down" arrow keys (located by the side of "Alignments to be concatenated"
30            list) before performing the actual concatenation.
31
32            Pressing CLEAR LIST button clears the alignments list selected for
33            concatenation.
34
35            Use "Alignment Separator" to specify the tag/separator to be inserted into the
36            target sequence data between the data of the alignments to be concatenated.
37
38            Pressing the "CONCATENATE" button performs a concatenation of the alignments
39            selected in the order given in the "Alignments to be concatenated" list.
40
41            Use the "MERGE SIMILAR SPECIES" button to create new species by merging similar
42            species (for e.g., similar species having different sequence alignments).
43            This function is also available from the Species menu.
44            See LINK{merge_species.hlp} for details.
45
46            If the database contains similar species with different sequence alignments
47            use "MERGE & CONCATENATE" button to generate new species by merging similar
48            species in the database and concatenating the different sequence alignments
49            contained in the newly merged species.
50
51NOTES
52
53            If problems occurs during "Merging similar species" and/or "Concatenation",
54            try the following -
55
56            1. Search the database for the "merged_species" field and mark the listed
57            species, if any, and delete them.
58
59            2. Then search the database for the <criterion_field> to use for merging
60            similar species. Mark the resulting species and perform merging similar
61            species.
62
63            3. Usually newly generated (merged) species are marked and use the same to
64            perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT
65            coinside with the selected alignments (names) to be concatenated!
66
67EXAMPLES        See LINK{gene_species.hlp}
68
69WARNINGS        None
70
71BUGS            No bugs known
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